Setting ploidy level in gatk

Question

[analyst]

Dear all,

i am working on sugarcane WGS analysis. I downloaded reference genome SofficinarumxspontaneumR570 from phytozomev13. In variant calling step i do not know which ploidy should i set in haplotypecaller as sugarcane is anueploid.

Please guide about ploidy level of sugarcane hybrid variety SofficinarumxspontaneumR570.

Thanks alot.

Answer 1

[GenoMax]

Have you seen: https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diploid-organisms

[analyst]

I will look into it thanks!